1. Transcription and Translation: Part 1 of 3: RNA Tsonwin Hai, Ph.D. Professor Department of Molecular and Cellular Biochemistry The Ohio State University College of Medicine

2. Study Objective At the end of this module, you should be able to: Understand the terms: Transcription, Translation, Splicing, Exon, Intron (removed), 5’-UTR, 3’-UTR, and ORF. Identify palindromic sequences. Know what mRNAs, tRNAs, rRNAs, and miRs are—in a broad sense. (You do not need to memorize the details; the details are provided via the links for your reference.) Identify RNA features from a list of multiple choices. Answer the practice exam questions (on the slides at the end). Textbook: Principles of Medical Biochemistry, Meisenberg and Simmons, Mosby, Inc. copyright 1998; Chapter 6, DNA, RNA, and Protein Synthesis (particularly pp85-86, 97-103)

3. Section I: Different RNAs Transcription: The process of making RNA using RNA polymerases. Take Home Message: The majority of cellular RNAs are engaged in protein synthesis. The main RNAs—mRNA, tRNA, and rRNA—are used as “software” and “hardware” for proteins synthesis and miRs are used to regulate this process. Translation: The process of making protein. In this process, mRNAs provide “messages” (genetic codes, an analogy as “software” in computer) to decide what proteins to make; tRNAs, and rRNAs form the major components of the protein synthesis machinery (“hardware” in computer) to produce the protein. Although some proteins (such as elongation factors and ribosomal proteins) are involved in this process, RNAs are the major components. miRs: miRNAs regulate the level of protein production by inhibiting translation or targeting mRNA for degradation. RNAs Messenger RNA (mRNA) Transfer RNA (tRNA) Ribosomal RNA (rRNA)—the most abundant RNA in cells microRNA (miRNA, also abbreviated as miR) Other types of RNAs: small nuclear RNA (such as snRNA), only in eukaryotes If you do not know the material well, click on the “Attachments” (on the upper right corner) for more information.

5. Section II: Features of RNAs RNA can contain modified bases. Although DNA can also be modified at the bases, its modification is not as varied as RNA. RNA is unstable (due to its 2'-OH). Most RNAs are single stranded. RNA can form secondary structures. That is, some segments of RNA can form base pairs with other segments of the same RNA molecules (intra-chain base pairing) due to the palindromic sequence. RNA molecules may form unusual base pairing: non-Watson-Crick base paring. RNA is made of four nucleotides (A, U, C, G), linked by phosphodiester bond. Unusual base pairings allow some RNA to form tertiary structures. The ability of RNA to form secondary and tertiary structures is the hallmark of RNA. If you know the material well, go ahead and take the quiz below. If you want to learn more about these, click the “Attachments” (on the upper right corner) for more information.

7. Drawing Exercise An RNA molecule with the palindromic sequence 5’- UCCUAXXXUAGGA-3’: What secondary structure (hairpin loop) will this molecule form? Draw a picture. 5’-UCCUAXXXUAGGA RADAR AGGAUXXXAUCCU-5’

8. Drawing Exercise An RNA molecule with the palindromic sequence 5’-UCCUAXXXUAGGA-3’: What secondary structure (hairpin loop) will this molecule form? Draw a picture. Answer:

9. Section III: A Few Terms When first synthesized, many eukaryotic RNAs contain segments of RNA that will be removed later. These segments are called the intervening sequences or introns. The remaining segments are called exons. The process of removing the introns is called splicing. Newly synthesized mRNA is called pre-mRNA; after processing, the mRNA is called mature mRNA. Only exons remain in the mature mRNA. Within the mature mRNA molecule, only a portion is used as templates to synthesize proteins (from the initiation codon to the termination codon). This portion is called open reading frame (ORF). Region upstream to ORF in the mature mRNA is called 5’-untranslated region (5’-UTR) and region down stream 3’-UTR. Note that splicing occurs in mRNA, tRNA, and rRNA. Intron, Exon, Splicing, ORF 5’-CAP structure, 3’-PolyA For eukaryotic mRNAs, its 5’ end is usually modified to form a so-called "CAP" structure (modified at the first base). For most of the eukaryotic mRNAs, their 3’-end is poly adenylated with a stretch of adenine residues (called PolyA tail). Thus, neither CAP nor poly (A) is encoded in the DNA (blueprint); rather they are added after the mRNA is synthesized.

10. 1 3 * 4 $ 2 In the figure below, boxes represent exons (1-4), lines introns, $ initiation codon, and * termination codon. Draw a picture of the mature mRNA and label its ORF, 5’-UTR and 3’-UTR. Drawing Exercise

11. 1 3 * 4 $ 2 In the figure below, boxes represent exons (1-4), lines introns, $ initiation codon, and * termination codon. Draw a picture of the mature mRNA and label its ORF, 5’-UTR and 3’-UTR. Drawing Exercise CAP Added All from exons PolyA Added 5'UTR3'UTR $ * CAP AAAA n AA OH 1234 ORF Answer:

13. Thank You If you have any questions, please contact me at hai.2@osu.edu.hai.2@osu.edu